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vortexR

An R package for Post Vortex Simulation Analysis.

Using this package, data of population viability analysis (PVA) generated with the software Vortex (Lacy & Pollak 2013) can be collated, plotted and analysed using basic (e.g. pairwise comparisons of scenarios) or more advanced statistics (e.g. fitting regression models).

Install

The stable version of vortexR can be installed with:

install.packages("vortexR", dependencies = TRUE)

The latest development versions of vortexR and its supplementary data package vortexRdata can be installed with:

# install.packages("devtools")
devtools::install_github("carlopacioni/vortexRdata")
devtools::install_github("carlopacioni/vortexR")

Fresh Windows installations of R will require Rtools for Windows.

If installation with build_vignette=TRUE fails, you can run install_github("carlopacioni/vortexR").

Java-based packages

The packages glmulti and rJava require a Java Development Kit (JDK) installed and registered correctly with R. Make sure to install a 64-bit JDK if you are using a 64-bit version of R.

A typical installation path for Java-based packages like glmulti in a GNU/Linux-based operating system (here: Ubuntu 16.04 LTS) along the lines of DigitalOcean’s tutorial:

Independently of vortexR, a sudo R CMD javareconf (and possibly the installation of rJava and Java-using packages like glmulti) will be required after each update of R and / or your Java installation.

A typical installation under Windows could follow:

If you have still problem installing and loading glmulti package and/or rJava, you may not have Java installed or are not using the same Java version as R. Make sure that if you are using a 64-bit version of R, you also have installed a 64 bit version of Java (most automatic installation via web browser will install a 32-bit version).

Your mileage may vary depending on your operating system and your versions of Java and R. Stack Overflow’s R community is a great source for troubleshooting.

Learn

Use ??vortexR to see a broad description of the package. Use help(package = "vortexR") to see the documentations available. Read the vignette for a more comprehensive description of the package. Be aware, if you did not use build_vignette=TRUE this documentation may not be available from within R. In these cases, download the PDF of these documents. On some platforms, ??vortexR may not work even if you used build_vignette=TRUE.

Use

If you use vortexR, please use the citation generated from citation('vortexR').

Contribute

We are happy to receive feedback and contributions through bug reports and pull requests.

We aim to follow the style suggestions by formatR::tidy_dir("R", width.cutoff = 79), lintr::lint_package(), and devtools::check(check_version = T, force_suggests = T, cran = T).

In a new environment, e.g. after an upgrade of R, running the tests could require to install vortexR’s dependencies with install.packages("vortexR", dependencies = T).

Note on R 3.4.0: update lintr to solve bug roxygen #627.